piggyback - Managing Larger Data on a GitHub Repository
Helps store files as GitHub release assets, which is a convenient way for large/binary data files to piggyback onto public and private GitHub repositories. Includes functions for file downloads, uploads, and managing releases via the GitHub API.
Last updated 4 months ago
data-storegit-lfspeer-reviewed
184 stars 12.85 score 24 dependencies 12 dependentsEML - Read and Write Ecological Metadata Language Files
Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.
Last updated 2 years ago
emleml-metadatametadata-standard
97 stars 11.18 score 46 dependencies 7 dependentsknitcitations - Citations for 'Knitr' Markdown Files
Provides the ability to create dynamic citations in which the bibliographic information is pulled from the web rather than having to be entered into a local database such as 'bibtex' ahead of time. The package is primarily aimed at authoring in the R 'markdown' format, and can provide outputs for web-based authoring such as linked text for inline citations. Cite using a 'DOI', URL, or 'bibtex' file key. See the package URL for details.
Last updated 4 years ago
219 stars 10.38 score 27 dependencies 4 dependentsRNeXML - Semantically Rich I/O for the 'NeXML' Format
Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.
Last updated 5 months ago
metadatanexmlphylogeneticslinked-data
13 stars 9.91 score 38 dependencies 18 dependentsrfishbase - R Interface to 'FishBase'
A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'
Last updated 1 months ago
fishfishbasetaxonomy
111 stars 9.68 score 31 dependencies 2 dependentscodemetar - Generate 'CodeMeta' Metadata for R Packages
The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides utilities to generate, parse, and modify 'codemeta.json' files automatically for R packages, as well as tools and examples for working with 'codemeta.json' 'JSON-LD' more generally.
Last updated 3 months ago
metadatacodemetaropenscicitationcreditlinked-datajson-ldpeer-reviewed
66 stars 9.15 score 41 dependencies 5 dependentsduckdbfs - High Performance Remote File System, Database and 'Geospatial' Access Using 'duckdb'
Provides friendly wrappers for creating 'duckdb'-backed connections to tabular datasets ('csv', parquet, etc) on local or remote file systems. This mimics the behaviour of "open_dataset" in the 'arrow' package, but in addition to 'S3' file system also generalizes to any list of 'http' URLs.
Last updated 1 months ago
68 stars 8.23 score 26 dependencies 16 dependentstaxadb - A High-Performance Local Taxonomic Database Interface
Creates a local database of many commonly used taxonomic authorities and provides functions that can quickly query this data.
Last updated 6 months ago
43 stars 7.88 score 37 dependencies 1 dependentsarkdb - Archive and Unarchive Databases Using Flat Files
Flat text files provide a robust, compressible, and portable way to store tables from databases. This package provides convenient functions for exporting tables from relational database connections into compressed text files and streaming those text files back into a database without requiring the whole table to fit in working memory.
Last updated 9 months ago
archivingdatabasedbipeer-reviewed
78 stars 7.34 score 1 dependenciesneonstore - NEON Data Store
The National Ecological Observatory Network (NEON) provides access to its numerous data products through its REST API, <https://data.neonscience.org/data-api/>. This package provides a high-level user interface for downloading and storing NEON data products. Unlike 'neonUtilities', this package will avoid repeated downloading, provides persistent storage, and improves performance. 'neonstore' can also construct a local 'duckdb' database of stacked tables, making it possible to work with tables that are far to big to fit into memory.
Last updated 6 months ago
databaseecologyneon-dataprovenance
8 stars 6.98 score 52 dependencies 11 dependentstreebase - Discovery, Access and Manipulation of 'TreeBASE' Phylogenies
Interface to the API for 'TreeBASE' <http://treebase.org> from 'R.' 'TreeBASE' is a repository of user-submitted phylogenetic trees (of species, population, or genes) and the data used to create them.
Last updated 8 months ago
10 stars 6.91 score 16 dependencies 2 dependentscodemeta - A Smaller 'codemetar' Package
The 'Codemeta' Project defines a 'JSON-LD' format for describing software metadata, as detailed at <https://codemeta.github.io>. This package provides core utilities to generate this metadata with a minimum of dependencies.
Last updated 11 months ago
metadatacodemetaropenscicitationcreditlinked-data
8 stars 5.97 score 4 dependencies 6 dependentssarsop - Approximate POMDP Planning Software
A toolkit for Partially Observed Markov Decision Processes (POMDP). Provides bindings to C++ libraries implementing the algorithm SARSOP (Successive Approximations of the Reachable Space under Optimal Policies) and described in Kurniawati et al (2008), <doi:10.15607/RSS.2008.IV.009>. This package also provides a high-level interface for generating, solving and simulating POMDP problems and their solutions.
Last updated 3 months ago
decision-theoryfisheriespomdp
9 stars 4.79 score 10 dependenciespmc - Phylogenetic Monte Carlo
Monte Carlo based model choice for applied phylogenetics of continuous traits. Method described in Carl Boettiger, Graham Coop, Peter Ralph (2012) Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. <doi:10.1111/j.1558-5646.2011.01574.x>.
Last updated 1 years ago
2 stars 4.60 score 64 dependenciesrgpdd - R Interface to the Global Population Dynamics Database
R Interface to the Global Population Dynamics Database (<https://ecologicaldata.org/wiki/global-population-dynamics-database>)
Last updated 4 years ago
10 stars 3.70 score 0 dependencies